Experimental and computational analysis of a large protein network that controls fat storage reveals the design principles of a signaling network.

PubWeight™: 0.76‹?›

🔗 View Article (PMC 4447291)

Published in PLoS Comput Biol on May 28, 2015

Authors

Bader Al-Anzi1, Patrick Arpp1, Sherif Gerges2, Christopher Ormerod3, Noah Olsman4, Kai Zinn1

Author Affiliations

1: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America.
2: Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America.
3: Division of Physics, Mathematics, and Astronomy, California Institute of Technology, Pasadena, California, United States of America.
4: Control and Dynamical Systems Option, Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, California, United States of America.

Articles cited by this

Collective dynamics of 'small-world' networks. Nature (1998) 98.45

Emergence of scaling in random networks Science (1999) 89.38

A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature (2000) 47.15

Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature (2002) 45.19

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66

A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A (2001) 33.71

Lethality and centrality in protein networks. Nature (2001) 29.64

Error and attack tolerance of complex networks Nature (2000) 27.90

Modularity and community structure in networks. Proc Natl Acad Sci U S A (2006) 17.97

The genetic landscape of a cell. Science (2010) 16.52

Resilience of the internet to random breakdowns Phys Rev Lett (2000) 8.00

Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46

Breakdown of the internet under intentional attack. Phys Rev Lett (2001) 6.00

A global protein kinase and phosphatase interaction network in yeast. Science (2010) 5.95

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol (2006) 5.57

An in vivo map of the yeast protein interactome. Science (2008) 5.52

Functional genomic screen reveals genes involved in lipid-droplet formation and utilization. Nature (2008) 4.70

Subnets of scale-free networks are not scale-free: sampling properties of networks. Proc Natl Acad Sci U S A (2005) 3.75

Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol (2004) 3.73

Up-to-date catalogues of yeast protein complexes. Nucleic Acids Res (2008) 3.69

How reliable are experimental protein-protein interaction data? J Mol Biol (2003) 3.59

Target of rapamycin (TOR) in nutrient signaling and growth control. Genetics (2011) 3.28

Genetic basis of mitochondrial function and morphology in Saccharomyces cerevisiae. Mol Biol Cell (2002) 3.27

The lipodystrophy protein seipin is found at endoplasmic reticulum lipid droplet junctions and is important for droplet morphology. Proc Natl Acad Sci U S A (2007) 3.11

Inhibitory effect of modified bafilomycins and concanamycins on P- and V-type adenosinetriphosphatases. Biochemistry (1993) 2.86

Fld1p, a functional homologue of human seipin, regulates the size of lipid droplets in yeast. J Cell Biol (2008) 2.85

Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PLoS Comput Biol (2007) 2.84

SNF1/AMPK pathways in yeast. Front Biosci (2008) 2.70

MEK inhibitors: the chemistry and biological activity of U0126, its analogs, and cyclization products. Bioorg Med Chem Lett (1998) 2.61

A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Mol Cell (2011) 2.55

COPI complex is a regulator of lipid homeostasis. PLoS Biol (2008) 2.47

Evolutionary and physiological importance of hub proteins. PLoS Comput Biol (2006) 2.34

The CCR4 gene from Saccharomyces cerevisiae is required for both nonfermentative and spt-mediated gene expression. Genetics (1990) 2.34

Assembly of scaffold-mediated complexes containing Cdc42p, the exchange factor Cdc24p, and the effector Cla4p required for cell cycle-regulated phosphorylation of Cdc24p. J Biol Chem (2000) 2.04

A genome-wide screen for regulators of TORC1 in response to amino acid starvation reveals a conserved Npr2/3 complex. PLoS Genet (2009) 1.64

An integrated approach to characterize genetic interaction networks in yeast metabolism. Nat Genet (2011) 1.62

How scale-free are biological networks. J Comput Biol (2006) 1.62

Mapping the cellular response to small molecules using chemogenomic fitness signatures. Science (2014) 1.39

Triacylglycerol homeostasis: insights from yeast. J Biol Chem (2010) 1.36

The uses of genome-wide yeast mutant collections. Genome Biol (2004) 1.36

The regulation of filamentous growth in yeast. Genetics (2012) 1.29

The powerful law of the power law and other myths in network biology. Mol Biosyst (2009) 1.29

Revealing the hidden language of complex networks. Sci Rep (2014) 1.25

The yeast deletion collection: a decade of functional genomics. Genetics (2014) 1.15

Genome wide expression analysis of the CCR4-NOT complex indicates that it consists of three modules with the NOT module controlling SAGA-responsive genes. Mol Genet Genomics (2008) 1.09

Flo11p, drug efflux pumps, and the extracellular matrix cooperate to form biofilm yeast colonies. J Cell Biol (2011) 1.08

V-ATPases as drug targets. J Bioenerg Biomembr (2005) 1.07

Color and contrast sensitivity in the lateral geniculate body and primary visual cortex of the macaque monkey. J Neurosci (1990) 1.05

Involvement of the nonhomologous region of subunit A of the yeast V-ATPase in coupling and in vivo dissociation. J Biol Chem (2004) 1.04

Glucose signaling-mediated coordination of cell growth and cell cycle in Saccharomyces cerevisiae. Sensors (Basel) (2010) 1.01

V-ATPase engagement in autophagic processes. Autophagy (2011) 0.98

A novel scoring approach for protein co-purification data reveals high interaction specificity. PLoS Comput Biol (2009) 0.98

Identification of inhibitors of vacuolar proton-translocating ATPase pumps in yeast by high-throughput screening flow cytometry. Anal Biochem (2009) 0.97

Colorimetric measurement of triglycerides cannot provide an accurate measure of stored fat content in Drosophila. PLoS One (2010) 0.96

Mechanism of action of CM-55, a synthetic analogue of the antilipogenic antibiotic cerulenin. Antimicrob Agents Chemother (1974) 0.94

Recent progress on the analysis of power-law features in complex cellular networks. Cell Biochem Biophys (2007) 0.91

Obese and anorexic yeasts: experimental models to understand the metabolic syndrome and lipotoxicity. Biochim Biophys Acta (2010) 0.89

Rho signaling participates in membrane fluidity homeostasis. PLoS One (2012) 0.87

Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation. BMC Syst Biol (2010) 0.86

Detection of locally over-represented GO terms in protein-protein interaction networks. J Comput Biol (2010) 0.85

Solution structure of a novel Cdc42 binding module of Bem1 and its interaction with Ste20 and Cdc42. J Biol Chem (2010) 0.82

Conditions with high intracellular glucose inhibit sensing through glucose sensor Snf3 in Saccharomyces cerevisiae. J Cell Biochem (2010) 0.82

Genome-wide screens for gene products regulating lipid droplet dynamics. Methods Cell Biol (2012) 0.81

How can yeast cells decide between three activated MAP kinase pathways? A model approach. J Theor Biol (2009) 0.79

Complementation and characterization of the Pneumocystis carinii MAPK, PCM. FEBS Lett (2003) 0.79

Modelling the yeast interactome. Sci Rep (2014) 0.78

Interaction networks: lessons from large-scale studies in yeast. Proteomics (2009) 0.77

Quantitative imaging of lipid metabolism in yeast: from 4D analysis to high content screens of mutant libraries. Methods Cell Biol (2012) 0.77

NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiae. Nucleic Acids Res (2012) 0.77

Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae. Mol Biosyst (2012) 0.76

Genetics of fat storage in flies and worms: what went wrong? Front Genet (2011) 0.76